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Serrano MJ, Goudet J, Cumer T. Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region. PLoS One 2024; 19:e0295595. [PMID: 38271341 PMCID: PMC10810427 DOI: 10.1371/journal.pone.0295595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/24/2023] [Indexed: 01/27/2024] Open
Abstract
Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.
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Affiliation(s)
- Marcelo J. Serrano
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Skorupski J, Brandes F, Seebass C, Festl W, Śmietana P, Balacco J, Jain N, Tilley T, Abueg L, Wood J, Sims Y, Formenti G, Fedrigo O, Jarvis ED. Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761. Int J Mol Sci 2023; 24:14816. [PMID: 37834264 PMCID: PMC10573602 DOI: 10.3390/ijms241914816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction.
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Affiliation(s)
- Jakub Skorupski
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Florian Brandes
- Wildtier- und Artenschutzstation e.V., Hohe Warte 1, 31553 Sachsenhagen, Germany
| | | | - Wolfgang Festl
- EuroNerz e.V., Kleine Gildewart 3, 49074 Osnabrück, Germany
| | - Przemysław Śmietana
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13 St., 71-415 Szczecin, Poland
- Polish Society for Conservation Genetics LUTREOLA, Maciejkowa 21 St., 71-784 Szczecin, Poland
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Nivesh Jain
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Tatiana Tilley
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Jonathan Wood
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Ying Sims
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
| | - Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA
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Gutiérrez EG, Ortega J, Savoie A, Baeza JA. The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates. BMC Genomics 2023; 24:527. [PMID: 37674108 PMCID: PMC10481570 DOI: 10.1186/s12864-023-09596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments. RESULTS The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4. CONCLUSION The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Avery Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Baeza JA, Macdonald-Shedd A, Latorre-Cárdenas MC, Griffin E, Gutiérrez-Rodríguez C. The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae. J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Forcina G, Camacho-Sanchez M, Cornellas A, Leonard JA. Complete mitogenomes reveal limited genetic variability in the garden dormouse Eliomys quercinus of the Iberian Peninsula. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The garden dormouse Eliomys quercinus is a poorly known Western Palearctic species experiencing a global decline. Even though the availability of genetic information is key to assess the driversunderlying demographic changes in wild populations and plan adequate management, data on E. quercinus are still scant. In this study, we reconstructed the complete mitogenomes of four E. quercinus individuals from southern Spain using in–solution enriched libraries, and found evidence of limited genetic variability. We then compared their cytochrome b sequences to those of conspecifics from other countries and supported the divergent but genetically depauperate position of this evolutionarily significant unit (ESU). The information produced will assist future conservation studies on this little–studied rodent.
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Affiliation(s)
- G. Forcina
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - M. Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - A. Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
| | - J. A. Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana, Sevilla, Spain
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